Structure of PDB 5z9q Chain A Binding Site BS02

Receptor Information
>5z9q Chain A (length=178) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDKEIIVTIHADNSVSVQ
DDGRGIPTGIHPEEGVSAAEVIMTVLGVGVSVVNALSQKLELVIQREGKI
HRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKR
LRELSFLNSGVSIRLRDKRDGKEDHFHY
Ligand information
Ligand IDAX7
InChIInChI=1S/C7H7N3/c8-7-9-5-3-1-2-4-6(5)10-7/h1-4H,(H3,8,9,10)
InChIKeyJWYUFVNJZUSCSM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1[nH]c2ccccc2n1
ACDLabs 10.04n2c1ccccc1nc2N
OpenEye OEToolkits 1.5.0c1ccc2c(c1)[nH]c(n2)N
FormulaC7 H7 N3
Name1H-benzimidazol-2-amine
ChEMBLCHEMBL305513
DrugBank
ZINCZINC000016889973
PDB chain5z9q Chain A Residue 305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5z9q Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes
Resolution1.8 Å
Binding residue
(original residue number in PDB)		R20 H147 E174
Binding residue
(residue number reindexed from 1)		R5 H107 E134
Annotation score1
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
Biological Process
GO:0006265 DNA topological change

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Molecular Function
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Biological Process
External links
PDB RCSB:5z9q, PDBe:5z9q, PDBj:5z9q
PDBsum5z9q
PubMed30429968
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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